[3] Whalen began his coaching career at Springfield College as a graduate assistant in football and wrestling.
[3] He was an assistant football coach at Williams College from 1996 to 2003, including three years as the team's offensive coordinator.
[3] Whalen served six years as Williams' head coach (2004–2009) during which he compiled a record of 38–10 (.792 winning percentage).
[3] In 2006, he led Williams to an undefeated, untied 8–0 record and the New England Small College Athletic Conference championship.
[2] In March 2010, Wesleyan hired Whalen as its head football coach and assistant athletic director.